Wow, major problems with Gnome and trying to change themes. Ended up the issue was some weird conflict with the gtk-qt-engine package. A simple:

apt-get remove –purge gtk-qt-engine

solved the problem. Of course it took a fews days of googling to find the answer, which was on Ubuntu’s bug tracker (don’t have the link handy sorry). The issue I had was that if I tried to change the theme or any part of the appearance of Gnome, the whole theming application would go blank. If you expierence this too, remove gtk-qt-engine .